Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,795,591	G→A	S221S (TCG→TCA)	waaF →	ADP‑heptose:LPS heptosyltransferase II

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,795,591	0	G	A	100.0%	282.5 / NA	79	S221S (TCG→TCA)	waaF	ADP‑heptose:LPS heptosyltransferase II
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (42/37);  total (42/37)

GGAGTTTGGTCCGGCAAAACGCTGGCCACACTACCACTATGCGGAGCTGGCAAAGCAGCTGATTGATGAAGGTTATCAGGTGGTTCTGTTTGGCTCGGCGAAAGATCATGAAGCGGGCAATGAGATTCTTGCCGCTTTGAATACCGAGCAGCAGGCATGGTGTCGGAACCTGGCGGGGGAAACACAGCTTGAT  >  NC_000913/3795495‑3795687                                                                                                 |                                                                                                 ggAGTTTGGTCCGGCAAAACGCTGGCCACACTACCACTATGCGGAGCTGGCAAAGCAGCTGATTGATGAAGGTTATCAGGTGGTTCTGTTTGGCTCAGCg                                                                                               <  2:913352/100‑1 (MQ=255) ggAGTTTGGTCCGGCAAAACGCTGGCCACACTACCACTATGCGGAGCTGGCAAAGCAGCTGATTGATGAAGGTTATCAGGTGGTTCTGTTTGGCTCAGCg                                                                                               >  2:2125990/1‑100 (MQ=255)     tttGGTCCGGCAAAACGCTGGCCACACTACCACTATGCGGAGCTGGCAAAGCAGCTGATTGATGAAGGTTATCAGGTGGTTCTGTTTGGCTCAGCGAAAg                                                                                           <  2:238113/100‑1 (MQ=255)      ttGGTCCGGCAAAACGCTGGCCACACTACCACTATGCGGAGCTGGCAAAGCAGCTGATTGATGAAGGTTATCAGGTGGTTCTGTTTGGCTCAGCGAAAGa                                                                                          <  2:283100/100‑1 (MQ=255)      ttGGTCCGGCAAAACGCTGGCCACACTACCACTATGCGGAGCTGGCAAAGCAGCTGATTGATGAAGGTTATCAGGTGGTTCTGTTTGGCTCAGCGAAAGa                                                                                          >  1:995013/1‑100 (MQ=255)        ggTCCGGCAAAACGCTGGCCACACTACCACTATGCGGAGCTGGCAAAGCAGCTGATTGATGAAGGTTATCAGGTGGTTCTGTTTGGCTCAGCGAAAGATc                                                                                        >  2:998932/1‑100 (MQ=255)        ggTCCGGCAAAACGCTGGCCACACTACCACTATGCGGAGCTGGCAAAGCAGCTGATTGATGAAGGTTATCAGGTGGTTCTGTTTGGCTCAGCGAAAGATc                                                                                        >  2:998914/1‑100 (MQ=255)         gTCCGGCAAAACGCTGGCCACACTACCACTATGCGGAGCTGGCAAAGCAGCTGATTGATGAAGGTTATCAGGTGGTTCTGTTTGGCTCAGCGAAAGATCa                                                                                       <  1:2125997/100‑1 (MQ=255)         gTCCGGCAAAACGCTGGCCACACTACCACTATGCGGAGCTGGCAAAGCAGCTGATTGATGAAGGTTATCAGGTGGTTCTGTTTGGCTCAGCGAAAGATCa                                                                                       <  1:1238303/100‑1 (MQ=255)         gTCCGGCAAAACGCTGGCCACACTACCACTATGCGGAGCTGGCAAAGCAGCTGATTGATGAAGGTTATCAGGTGGTTCTGTTTGGCTCAGCGAAAGATCa                                                                                       <  1:1839835/100‑1 (MQ=255)         gTCCGGCAAAACGCTGGCCACACTACCACTATGCGGAGCTGGCAAAGCAGCTGATTGATGAAGGTTATCAGGTGGTTCTGTTTGGCTCAGCGAAAGATCa                                                                                       >  1:1298500/1‑100 (MQ=255)           ccGGCAAAACGCTGGCCACACTACCACTATGCGGAGCTGGCAAAGCAGCTGATTGATGAAGGTTATCAGGTGGTTCTGTTTGGCTCAGCGAAAGATCATg                                                                                     >  1:948461/1‑100 (MQ=255)           ccGGCAAAACGCTGGCCACACTACCACTATGCGGAGCTGGCAAAGCAGCTGATTGATGAAGGTTATCAGGTGGTTCTGTTTGGCTCAGCGAAAGATCATg                                                                                     <  2:1834592/100‑1 (MQ=255)            cGGCAAAACGCTGGCCACACTACCACTATGCGGAGCTGGCAAAGCAGCTGATTGATGAAGGTTATCAGGTGGTTCTGTTTGGCTCAGCGAAAGATCATGa                                                                                    <  2:1946436/100‑1 (MQ=255)            cGGCAAAACGCTGGCCACACTACCACTATGCGGAGCTGGCAAAGCAGCTGATTGATGAAGGTTATCAGGTGGTTCTGTTTGGCTCAGCGAAAGATCATGa                                                                                    <  2:2230217/100‑1 (MQ=255)             ggCAAAACGCTGGCCACACTACCACTATGCGGAGCTGGCAAAGCAGCTGATTGATGAAGGTTATCAGGTGGTTCTGTTTGGCTCAGCGAAAGATCATGaa                                                                                   >  2:1436733/1‑100 (MQ=255)             ggCAAAACGCTGGCCACACTACCACTATGCGGAGCTGGCAAAGCAGCTGATTGATGAAGGTTATCAGGTGGTTCTGTTTGGCTCAGCGAAAGATCATGaa                                                                                   >  2:1302865/1‑100 (MQ=255)             ggCAAAACGCTGGCCACACTACCACTATGCGGAGCTGGCAAAGCAGCTGATTGATGAAGGTTATCAGGTGGTTCTGTTTGGCTCAGCGAAAGATCATGaa                                                                                   >  2:107812/1‑100 (MQ=255)             ggCAAAACGCTGGCCACACTACCACTATGCGGAGCTGGCAAAGCAGCTGATTGATGAAGGTTATCAGGTGGTTCTGTTTGGCTCAGCGAAAGATCATGaa                                                                                   >  1:882542/1‑100 (MQ=255)              gCAAAACGCTGGCCACACTACCACTATGCGGAGCTGGCAAAGCAGCTGATTGATGAAGGTTATCAGGTGGTTCTGTTTGGCTCAGCGAAAGATCATGAAg                                                                                  >  1:237273/1‑100 (MQ=255)               cAAAACGCTGGCCACACTACCACTATGCGGAGCTGGCAAAGCAGCTGATTGATGAAGGTTATCAGGTGGTTCTGTTTGGCTCAGCGAAAGATCATGAAGc                                                                                 >  2:1005888/1‑100 (MQ=255)                 aaaCGCTGGCCACACTACCACTATGCGGAGCTGGCAAAGCAGCTGATTGATGAAGGTTATCAGGTGGTTCTGTTTGGCTCAGCGAAAGATCATGAAGCgg                                                                               <  2:2148667/100‑1 (MQ=255)                 aaaCGCTGGCCACACTACCACTATGCGGAGCTGGCAAAGCAGCTGATTGATGAAGGTTATCAGGTGGTTCTGTTTGGCTCAGCGAAAGATCATGAAGCgg                                                                               <  2:2148739/100‑1 (MQ=255)                 aaaCGCTGGCCACACTACCACTATGCGGAGCTGGCAAAGCAGCTGATTGATGAAGGTTATCAGGTGGTTCTGTTTGGCTCAGCGAAAGATCATGAAGCgg                                                                               >  1:883172/1‑100 (MQ=255)                  aaCGCTGGCCACACTACCACTATGCGGAGCTGGCAAAGCAGCTGATTGATGAAGGTTATCAGGTGGTTCTGTTTGGCTCAGCGAAAGATCATGAAGCggg                                                                              <  1:1303057/100‑1 (MQ=255)                  aaCGCTGGCCACACTACCACTATGCGGAGCTGGCAAAGCAGCTGATTGATGAAGGTTATCAGGTGGTTCTGTTTGGCTCAGCGAAAGATCATGAAGCggg                                                                              <  1:2273658/100‑1 (MQ=255)                   aCGCTGGCCACACTACCACTATGCGGAGCTGGCAAAGCAGCTGATTGATGAAGGTTATCAGGTGGTTCTGTTTGGCTCAGCGAAAGATCATGAAGCGGGc                                                                             <  1:1088164/100‑1 (MQ=255)                   aCGCTGGCCACACTACCACTATGCGGAGCTGGCAAAGCAGCTGATTGATGAAGGTTATCAGGTGGTTCTGTTTGGCTCAGCGAAAGATCATGAAGCGGGc                                                                             <  2:883170/100‑1 (MQ=255)                       tGGCCACACTACCACTATGCGGAGCTGGCAAAGCAGCTGATTGATGAAGGTTATCAGGTGGTTCTGTTTGGCTCAGCGAAAGATCATGAAGCGGGCAATg                                                                         >  1:1279954/1‑100 (MQ=255)                        ggCCACACTACCACTATGCGGAGCTGGCAAAGCAGCTGATTGATGAAGGTTATCAGGTGGTTCTGTTTGGCTCAGCGAAAGATCATGAAGCGGGCAATga                                                                        >  1:835534/1‑100 (MQ=255)                             cacTACCACTATGCGGAGCTGGCAAAGCAGCTGATTGATGAAGGTTATCAGGTGGTTCTGTTTGGCTCAGCGAAAGATCATGAAGCGGGCAATGAGATTc                                                                   >  2:803043/1‑100 (MQ=255)                                tACCACTATGCGGAGCTGGCAAAGCAGCTGATTGATGAAGGTTATCAGGTGGTTCTGTTTGGCTCAGCGAAAGATCATGAAGCGGGCAATGAGATTCTTg                                                                <  1:1148010/100‑1 (MQ=255)                                    aCTATGCGGAGCTGGCAAAGCAGCTGATTGATGAAGGTTATCAGGTGGTTCTGTTTGGCTCAGCGAAAGATCATGAAGCGGGCAATGAGATTCTTGCCGc                                                            >  1:1078132/1‑100 (MQ=255)                                     cTATGCGGAGCTGGCAAAGCAGCTGATTGATGAAGGTTATCAGGTGGTTCTGTTTGGCTCAGCGAAAGATCATGAAGCGGGCAATGAGATTCTTGCCGCt                                                           <  2:390726/100‑1 (MQ=255)                                        tGCGGAGCTGGCAAAGCAGCTGATTGATGAAGGTTATCAGGTGGTTCTGTTTGGCTCAGCGAAAGATCATGAAGCGGGCAATGAGATTCTTGCCGCTTTg                                                        <  1:1436737/100‑1 (MQ=255)                                        tGCGGAGCTGGCAAAGCAGCTGATTGATGAAGGTTATCAGGTGGTTCTGTTTGGCTCAGCGAAAGATCATGAAGCGGGCAATGAGATTCTTGCCGCTTTg                                                        <  1:1302868/100‑1 (MQ=255)                                        tGCGGAGCTGGCAAAGCAGCTGATTGATGAAGGTTATCAGGTGGTTCTGTTTGGCTCAGCGAAAGATCATGAAGCGGGCAATGAGATTCTTGCCGCTTTg                                                        <  2:2322998/100‑1 (MQ=255)                                           cgatcTGGCAAAGCAGCTGATTGATGAAGGTTATTAGGTGGTTCTGTTTGGCTCAGCGAAAGATCATGAAGCGGGCAATGAGATTCTTTCCGATTTGAAt                                                     <  2:1233380/96‑1 (MQ=255)                                           cgatcTGGCAAAGCAGCTGATTGATGAAGGTTATCAGGTGGTTCTGTTTGGCTCAGCGAAAGATCATGAAGCGGGCAATGAGATTCTTGCCGCTTTGAAt                                                     <  2:1174799/96‑1 (MQ=255)                                             aGCTGGCAAAGCAGCTGATTGATGAAGGTTATCAGGTGGTTCTGTTTGGCTCAGCGAAAGATCATGAAGCGGGCAATGAGATTCTTGCCGCTTTGAATAc                                                   <  2:1020704/100‑1 (MQ=255)                                              gCTGGCAAAGCAGCTGATTGATGAAGGTTATCAGGTGGTTCTGTTTGGCTCAGCGAAAGATCATGAAGCGGGCAATGAGATTCTTGCCGCTTTGAATAcc                                                  <  1:249646/100‑1 (MQ=255)                                                tGGCAAAGCAGCTGATTGATGAAGGTTATCAGGTGGTTCTGTTTGGCTCAGCGAAAGATCATGAAGCGGGCAATGAGATTCTTGCCGCTTTGAATACCg                                                 >  2:2141978/1‑99 (MQ=255)                                                 ggCAAAGCAGCTGATTGATGAAGGTTATCAGGTGGTTCTGTTTGGCTCAGCGAAAGATCATGAAGCGGGCAATGAGATTCTTGCCGCTTTGAATagatcg                                               >  1:1174802/1‑95 (MQ=255)                                                 ggCAAAGCAGCTGATTGATGAAGGTTATCAGGTGGTTCTGTTTGGCTCAGCGAAAGATCATGAAGCGGGCAATGAGATTCTTGCCGCTTTGAATACCGag                                               >  1:2318594/1‑100 (MQ=255)                                                 ggCAAAGAAGCTGATTGATGAAGGTTATCAGGTGGTTCTGTTTGGCTCAGCGAAAGATCATGAAGCGGGCAATGAGATTCTTGCCGCTTTGAATagatcg                                               >  1:1233383/1‑95 (MQ=255)                                                   cAAAGCAGCTGATTGATGAAGGTTATCAGGTGGTTCTGTTTGGCTCAGCGAAAGATCATGAAGCGGGCAATGAGATTCTTGCCGCTTTGAATACCGatct                                             >  2:226107/1‑97 (MQ=255)                                                   cAAAGCAGCTGATTGATGAAGGTTATCAGGTGGTTCTGTTTGGCTCAGCGAAAGATCATGAAGCGGGCAATGAGATTCTTGCCGCTTGGAATACCGagca                                             >  1:689523/1‑100 (MQ=255)                                                     aaGCAGCTGATTGATGAAGGTTATCAGGTGGTTCTGTTTGGCTCAGCGAAAGATCATGAAGCGGGCAATGAGATTCTTGCCGCTTTGAATACCGagcagc                                           >  2:1902707/1‑100 (MQ=255)                                                         ctcTGATTGATGAAGGTTATCAGGTGGTTCTGTGTGGCTCAGCGAAAGATCATGAAGCGGGCAATGAGATTCTTGCCGCTTTGAATACCGAGCAGCAGGc                                       <  2:253538/98‑1 (MQ=255)                                                         agcTGATTGATGAAGGTTATCAGGTGGTTCTGTTTGGCTCAGCGAAAGATCATGAAGCGGGCAATGAGATTCTTGCCGCTTTGAATACCGAGCAGCAGGc                                       >  1:1864544/1‑100 (MQ=255)                                                          gcTGATTGATGAAGGTTATCAGGTGGTTCTGTTTGGCTCAGCGAAAGATCATGAAGCGGGCAATGAGATTCTTGCCGCTTTGAATACCGAGCAGCAggaa                                      <  1:1573603/100‑3 (MQ=255)                                                           cTGATTGATGAAGGTTATCAGGTGGTTCTGTTTGGCTCAGCGAAAGATCATGAAGCGGGCAATGAGATTCTTGCCGCTTTGAATACCGAGCAGCAGGCag                                     >  1:253540/1‑99 (MQ=255)                                                           cTGATTGATGAAGGTTATCAGGTGGTTCTGTTTGGCTCAGCGAAAGATCATGAAGCGGGCAATGAGATTCTTGCCGCTTTGAATACCGAGCAGCAGGCAt                                     >  2:1001534/1‑100 (MQ=255)                                                             gattgatGAAGGTTATCAGGTGGTTCTGTTTGGCTCAGCGAAAGATCATGAAGCGGGCAATGAGATTCTTGCCGCTTTGAATACCGAGCAGCAGGCATgg                                   <  2:802160/100‑1 (MQ=255)                                                             gattgatGAAGGTTATCAGGTGGTTCTGTTTGGCTCAGCGAAAGATCATGAAGCGGGCAATGAGATTCTTGCCGCTTTGAATACCGAGCAGCAGGCATgg                                   >  2:1152356/1‑100 (MQ=255)                                                             gattgatGAAGGTTATCAGGTGGTTCTGTTTGGCTCAGCGAAAGATCATGAAGCGGGCAATGAGATTCTTGCCGCTTTGAATACCGAGCAGCAGGCATgg                                   <  1:2090336/100‑1 (MQ=255)                                                             gattgatGAAGGTTATCAGGTGGTTCTGTTTGGCTCAGCGAAAGATCATGAAGCGGGCAATGAGATTCTTGCCGCTTTGAATACCGAGCAGCAGGCATgg                                   <  1:2195345/100‑1 (MQ=255)                                                                 gatgaAGGTTATCAGGTGGTTCTGTTTGGCTCAGCGAAAGATCATGAAGCGGGCAATGAGATTCTTGCCGCTTTGAATACCGAGCAGCAGGCATGgtgt                                >  1:408912/1‑99 (MQ=255)                                                                 gatgaAGGTTATCAGGTGGTTCTGTTTGGCTCAGCGAAAGATCATGAAGCGGGCAATGAGATTCTTGCCGCTTTGAATACCGAGCAGCAGGCATGGTGTc                               <  2:882540/100‑1 (MQ=255)                                                                  atgaAGGTTATCAGGTGGTTCTGTTTGGCTCAGCGAAAGATCATGAAGCGGGCAATGAGATTCTTGCCGCTTTGAATACCGAGCAGCAGGCATGGTGTCg                              >  1:1147341/1‑100 (MQ=255)                                                                   tgaAGGTTATCAGGTGGTTCTGTTTGGCTCAGCGAAAGATCATGAAGCGGGCAATGAGATTCTTGCCGCTTTGAATACCGAGCAGCAGGCATGGTGTCgg                             >  2:487339/1‑100 (MQ=255)                                                                   tgaAGGTTATCAGGTGGTTCTGTTTGGCTCAGCGAAAGATCATGAAGCGGGCAATGAGATTCTTGCCGCTTTGAATACCGAGCAGCAGGCATGGTGTCgg                             >  2:1381488/1‑100 (MQ=255)                                                                      aGGTTATCAGGTGGTTCTGTTTGGCTCAGCGAAAGATCATGAAGCGGGCAATGTGATTCTTGCCGCTTTGAATACCGAGCAGCAGGCATGGTGTCGGAAc                          <  2:1298497/100‑1 (MQ=255)                                                                        gTTATCAGGTGGTTCTGTTTGGCTCAGCGAAAGATCATGAAGCGGGCAATGAGATTCTTGCCGCTTTGAATACCGAGCAGCAGGCATGGTGTCGGAACCt                        <  2:1914426/100‑1 (MQ=255)                                                                         ttATCAGGTGGTTCTGTTTGGCTCAGCGAAAGATCATGAAGCGGGCAATGAGATTCTTGCCGCTTTGAATACCGAGCAGCAGGCATGGTGTCGGAACCt                        >  2:822436/1‑99 (MQ=255)                                                                              aGGTGGTTCTGTTTGGCTCAGCGAAAGATCATGAAGCGGGCAATGAGATTCTTGCCGCTTTGAATACCGAGCAGCAGGCATGGTGTCGGAACCTGGCggg                  >  1:113504/1‑100 (MQ=255)                                                                              aGGTGGTTCTGTTTGGCTCAGCGAAAGATCATGAAGCGGGCAATGAGATTCTTGCCGCTTTGAATACCGAGCAGCAGGCATGGTGTCGGAACCTGGCggg                  >  1:113050/1‑100 (MQ=255)                                                                               ggtggtTCTGTTTGGCTCAGCGAAAGATCATGAAGCGGGCAATGAGATTCTTGCCGCTTTGAATACCGAGCAGCAGGCATGGTGTCGGAACCTGGCgggg                 <  2:237271/100‑1 (MQ=255)                                                                               ggtggtTCTGTTTGGCTCAGCGAAAGATCATGAAGCGGGCAATGAGATTCTTGCCGCTTTGAATACCGAGCAGCAGGCATGGTGTCGGAACCTGGCgggg                 <  2:689522/100‑1 (MQ=255)                                                                                gtggtTCTGTTTGGCTCAGCGAAAGATCATGAAGCGGGCAATGAGATTCTTGCCGCTTTGAATACCGAGCAGCAGGCATGGTGTCGGAACCTGGCggggg                >  1:1160756/1‑100 (MQ=255)                                                                                   gtTCTGTTTGGCTCAGCGAAAGATCATGAAGCGGGCAATGAGATTCTTGCCGCTTTGAATACCGAGCAGCAGGCATGGTGTCGGAACCTGGCGGGGGaaa             >  1:588874/1‑100 (MQ=255)                                                                                    ttCTGTTTGGCTCAGCGAAAGATCATGAAGCGGGCAATGAGATTCTTGCCGCTTTGAATACCGAGCAGCAGGCATGGTGTCGGAACCTGGCGGGGGAAac            >  1:325999/1‑100 (MQ=255)                                                                                          ttGGCTCAGCGAAAGATCATGAAGCGGGCAATGAGATTCTTGCCGCTTTGAATACCGAGCAGCAGGCATGGTGTCGGAACCTGGCGGGGGAAACACAGCt      <  1:1858151/100‑1 (MQ=255)                                                                                           tGGCTCAGCGACCGATCATGAAGCGGGCAATGAGATTCTTGCAGCTTTGAATACCGAGCAGCAGGCATGGTGTCGGAACCTGGCGGGTGAAACACAGcgt     <  2:1013136/100‑3 (MQ=255)                                                                                           tGGCTCAGCGAAAGATCATGAAGCGGGCAATGAGATTCTTGCCGCTTTGAATACCGAGCAGCAGGCATGGTGTCGGAACCTGGCGGGGGAAACACAGCtt     >  1:980547/1‑100 (MQ=255)                                                                                            ggCTCAGCGAAAGATCATGAAGCGGGCAATGAGATTCTTGCCGCTTTGAATACCGAGCAGCAGGCATGGTGTCGGAACCTGGCGGGGGAAACACAGCTTg    <  2:2318585/100‑1 (MQ=255)                                                                                            ggCTCAGCGAAAGATCATGAAGCGGGCAATGAGATTCTTGCCGCTTTGAATACCGAGCAGCAGGCATGGTGTCGGAACCTGGCGGGGGAAACACAGCTTg    >  1:1897484/1‑100 (MQ=255)                                                                                             gCTCAGCGAAAGATCATGAAGCGGGCAATGAGATTCTTGCCGCTTTGAATACCGAGCAGCAGGCATGGTGTCGGAACCTGGCGGGGGAAACACAGCTTGa   >  1:2189741/1‑100 (MQ=255)                                                                                              cTCAGCGAAAGATCATGAAGCGGGCAATGAGATTCTTGCCGCTTTGAATACCGAGCAGCAGGCATGGTGTCGGAACCTGGCGGGGGAAACACAGCTTGAt  >  2:1261392/1‑100 (MQ=255)                                                                                                 |                                                                                                 GGAGTTTGGTCCGGCAAAACGCTGGCCACACTACCACTATGCGGAGCTGGCAAAGCAGCTGATTGATGAAGGTTATCAGGTGGTTCTGTTTGGCTCGGCGAAAGATCATGAAGCGGGCAATGAGATTCTTGCCGCTTTGAATACCGAGCAGCAGGCATGGTGTCGGAACCTGGCGGGGGAAACACAGCTTGAT  >  NC_000913/3795495‑3795687

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑